README -- Describes contents of HEMCO/GMI/v2015-02 directory 20 Apr 2018 GEOS-Chem Support Team geos-chem-support@g.harvard.edu Overview: =============================================================================== This directory contains the input files for applying linearized stratospheric chemistry production and loss in HEMCO. Each netcdf file contains the following variables (shown here for NO): > ncdump -h gmi.clim.NO.geos5.2x25 netcdf gmi.clim.NO.geos5.2x25 { dimensions: lon = 144 ; lat = 91 ; lev = 72 ; time = UNLIMITED ; // (12 currently) variables: float lon(lon) ; lon:standard_name = "longitude" ; lon:long_name = "longitude" ; lon:units = "degrees_east" ; lon:axis = "X" ; float lat(lat) ; lat:standard_name = "latitude" ; lat:long_name = "latitude" ; lat:units = "degrees_north" ; lat:axis = "Y" ; double lev(lev) ; lev:long_name = "GEOS-Chem level" ; lev:units = "level" ; lev:positive = "up" ; lev:axis = "Z" ; double time(time) ; time:standard_name = "time" ; time:long_name = "Time" ; time:units = "hours since 2005-01-01 00:00:00" ; time:calendar = "standard" ; float loss(time, lev, lat, lon) ; loss:long_name = "NO loss frequency" ; loss:units = "s^-1" ; float prod(time, lev, lat, lon) ; prod:long_name = "NO production rate" ; prod:units = "v/v/s" ; float species(time, lev, lat, lon) ; species:units = "v/v" ; species:lon_name = "NO mixing ratio" ; // global attributes: :CDI = "Climate Data Interface version 1.6.4 (http://code.zmaw.de/projects/cdi)" ; :Conventions = "CF-1.4" ; :history = "Fri Feb 06 11:25:07 2015: cdo setrtoc,1.0e-99,1.0e-30,0 gmi.clim.NO.geos5.2x25.nc tmp.nc\n", "Created by Christoph Keller: Fri Feb 6 11:25:02 EST 2015" ; :description = "Production rates and loss frequencies from the GMI combo model" ; :CDO = "Climate Data Operators version 1.6.4 (http://code.zmaw.de/projects: } They are the 3D climatological monthly mean production rates, loss frequencies, and concentrations for each species simulated by the GMI "Combo" model. GMI archives the reaction rates for each kinetic and photolysis reaction, which have been stoichiometrically summed for each individual species, and averaged over all years by L. Murray (ltmurray@post.harvard.edu) In addition to individual species, prod rates and loss frequencies were determined for the NOx family (= N + NO + NO2 + NO3 + HNO2 ) and Ox family (= O + O1D + O3). Ox was determined for completeness, only Linoz or Synoz are actually used by or recommended for GEOS-Chem. The GEOS-5X/MERRA files are the 2004-2010 monthly means from archived GMI output at ftp://dirac.gsfc.nasa.gov/pub/gmidata2/users/steenrod/MERRA The files and GMI stratospheric chemistry scheme are described in detail on the GEOS-Chem wiki page at http://wiki.seas.harvard.edu/geos-chem/index.php/Stratospheric_chemistry Files: =============================================================================== gmi.clim.*.geos5.2x25.nc -- Files containing the production, loss, and concentration (see above for ncdump output) for each of the species listed below. These were taken from the GMI Combi model. Species: A3O2 ACET ACTA ALD2 ALK4 ATO2 B3O2 Br BrCl BrO BrONO2 C2H6 C3H8 CCl4 CF2Br2 CF2Cl2 CF2ClBr CF3Br CFC113 CFC114 CFC115 CFCl3 CH2O CH3Br CH3CCl3 CH3Cl CH4 CO Cl Cl2 Cl2O2 ClO ClONO2 EOH ETO2 ETP GCO3 GLYC GLYX GP GPAN H H2 H2402 H2O H2O2 HAC HBr HCFC141b HCFC142b HCFC22 HCOOH HCl HNO2 HNO3 HNO4 HO2 HOBr HOCl IALD IAO2 IAP INO2 INPN ISN1 ISNP ISOP KO2 MACR MAN2 MAO3 MAOP MAP MCO3 MEK MGLY MO2 MOH MP MRO2 MRP MVK MVN2 N N2O N2O5 NO NO2 NO3 NOx O O1D O3 OClO OH Ox PAN PMN PO2 PP PPN PRN1 PRPE PRPN R4N1 R4N2 R4O2 R4P RA3P RB3P RCHO RCO3 RCOOH RIO1 RIO2 RIP ROH RP VRO2 VRP Addendum (20 Apr 2018): ------------------------------------------------------------------------------- NOTE: We have chunked all of the files in the HEMCO/GMI/v2015-02 directory so that they can be more efficiently read from disk by GCHP. We have also compressed them using netCDF deflation level 1. The following command was used: nccopy -c lon/144,lat/91,lev/1,time/1 -d1 Addendum (28 Oct 2016): ------------------------------------------------------------------------------- NOTE: We have added the file gmi.clim.HCOOH.geos5.2x25.20160912.nc Eloise Marais wrote: I ran GEOS-Chem with the GMI HCOOH prod/loss rates and had a large enhancement in HCOOH in February in the midlatitiudes. It's an isolated band that will presumably shift with time. I eventually found that it's because GMI stratosphere prod rates far exceed the loss rates. This likely isn't an issue in earlier versions of the model that didn't have GMI prod/loss rates for HCOOH. Xin Chen in Dylan Millet's group has an updated file of HCOOH GMI prod/ loss rates that should be used instead of the current prod/loss rates. Addendum (09 Jan 2017): ------------------------------------------------------------------------------- NOTE: We have added the file gmi.clim.HCOOH.geos5.2x25.20170108.nc Seb Eastham wrote: It looks like the values for the “time” variable in the GMI prod/loss file for HCOOH are not set correctly. Specifically the file gmi.clim.HCOOH.geos5.2x25.nc has the following entries for its time vector: time = 0,744,0,0,0,0,0,0,0,0,0,0 It should instead be: time = 0,744,1416,2160,2880,3624,4344,5088,5832,6552,7296,8016 This doesn’t cause a problem for HEMCO, but GCHP expects the time entries to be accurate and chokes on this file (by design). Would it be possible to update the file accordingly? I should point out that the alternative file (gmi.clim.HCOOH.geos5.2x25.20160912.nc) has the same problem. [Also ...] it looks like there is now another problem with the GMI HCOOH loss/prod frequencies, specifically with the dimension information. I noticed that there were significantly more dimension variables than had previously been the case, and this was causing dimension identification issues [in GCHP]....I also generated a simpler file, using the ISOP prod/loss frequency file as a template (as all the other GMI files are much simpler than the new HCOOH file) and writing the HCOOH loss/prod/species variables into it. Would it be possible to upload this as an alternative to the 20170103 file? I’ve successfully tested this one with GCHP, and all the other GMI prod/loss files also work with GCHP. Therefore, we have fixed the timestamps and have saved a new file called gmi.clim.HCOOH.geos5.2x25.20170108.nc. This contains the same prod/loss data as in gmi.clim.HCOOH.geos5.2x25.20160912.nc (i.e. Xin Chen's updated), but with the corrected timestamps. References: ================================================================================ GEOS-Chem Implementation: Murray, L. T., J. A. Logan, and D. J. Jacob, "Interannual variability in tropical tropospheric ozone and OH: the role of lightning", __J. Geophys. Res.__, 118, 1-13, doi:10.1002/jgrd.50857, 2013. Murray, L. T., D. J. Jacob, J. A. Logan, R. C. Hudman, and W. J. Koshak, "Optimized regional and interannual variability of lightning in a global chemical transport model constrained by LIS/OTD satellite data", __J. Geophys. Res.__, 117, D20307, doi:10.1029/2012JD017934, 2012. GMI Combo Model: Allen, D., K. Pickering, B. Duncan, and M. Damon (2010), "Impact of lightning NO emissions on North American photochemistry as determined using the Global Modeling Initiative (GMI) model", __J Geophys Res-Atmos__, 115, doi: 10.1029/2010JD014062. Considine, D. B., J. A. Logan, and M. A. Olsen (2008), "Evaluation of near-tropopause ozone distributions in the Global Modeling Initiative combined stratosphere/ troposphere model with ozonesonde data, __Atmos Chem Phys, 8(9)__, 2365–2385. Duncan, B. N., J. A. Logan, I. Bey, I. A. Megretskaia, R. M. Yantosca, Novelli, P. C., N. B. Jones, and C. P. Rinsland (2007), "Global budget of CO, 1988-1997: Source estimates and validation with a global model, __J Geophys Res-Atmos__, 112, doi: 10.1029/2007JD008459.